Report with R Markdown - Theory

1 Introduction

R Markdown is an authoring framework for data science (AFDS) combining R code with narrative text. AFDS are used to create data-driven documents (reports) with a notebook interface.

AFDS	Language	Description
Rmarkdown	R	front-end oriented
Jupyter	Python	back-end oriented
D3.js	JavaScript	web oriented
Plotly	JavaScript	web oriented

R Markdown is often enough for academic writing. It uses Markdown syntax, supports HTML/CSS markup languages, BibTex references, 3D plots, interactive maps. The main R Markdown packages are:

{knitr} engine for dynamic report generation with R (e.g. convert to LaTeX)
{rmarkdown} convert R Markdown documents into a variety of formats, extension of {knitr}
{tinytex} typesetting system for LaTeX syntax (e.g. export in PDF)
{bookdown} advanced editing and publishing functions (e.g. cross reference figures)

1.1 Create a new document

In RStudio:
File > New file > R Markdown...

The options (Title, Author) can be changed later on the YAML header. Let HTML as the default output format.

A new document is created:

Run the new document with knit, it will launch the render

1.2 Navigate

Use RStudio tools

knit when save the document

check spelling

knit the document

run Visual R Markdown + other options

new editing tools

create a new code chunk (R, Bash, D3, Python, etc.)

run a part or the whole document

publish the document

run Visual R Markdown

1.2.1 Visual R Markdown

Visual R Markdown as a Pandoc syntax (extension of Mardown), supports Zotero, can retrieve complete bibliographical references from DOI or searches on PubMed, Crossref, and DataCite

2 Document structure

R Markdown combines:

a YAML header for the document metadata
different code chunks (R code embedded)
many narrative parts (Markdown syntax) with inline R code

YAML header

narrative part

R code

narrative part

R code

…

2.1 Narrative parts

Narrative parts required principally the use of the Markdown syntax, but also supports HTML/CSS code, LaTeX syntax, etc.

2.1.1 Markdown syntax

Markdown is an easy-to-write plain text syntax used by different code-oriented frameworks:

Markdown basic syntax and Markdown online editor

Pandoc converter is an extension of Markdown, really usefull for text conversions (Markdown to HTML, LaTex to Markdown, etc.)

Styling text

code in R Markdown	Render
`bold, __bold__`	bold, bold
`italic, _italic_`	italic, italic
`code`	`code`
`hyphen -- inserted -- in a sentence`	hyphen – inserted – in a sentence
`H~2~O`	H₂O
`10^−19^`	10⁻¹⁹
`$$\sum_{i=1}^{n} X^3_i$$`	\[\sum_{i=1}^{n} X^3_i\]
…	…

blockquotes >

> I am a blockquote

I am a blockquote

line separator

--- or ***

A extended part of the text styling can also be done with HTML/CSS

Lists

- numbered  
  
  1. first element
  2. second element
  3. third element

numbered
1. first element
2. second element
3. third element

- bullet
  
  * first element
  * second element
  * third element
    - third element - sub 1
    - third element - sub 2
      + third element - sub 2 - subsub 1
      + third element - sub 2 - subsub 2

bullet
- first element
- second element
- third element
  - third element - sub 1
  - third element - sub 2
    - third element - sub 2 - subsub 1
    - third element - sub 2 - subsub 2

Tables

simple table

| Syntax | Description |
| --- | ----------- |
| Header | Title |
| Paragraph | Text |

and

| Syntax      | Description |
| ----------- | ----------- |
| Header      | Title       |
| Paragraph   | Text        |

produce the same result:

Syntax	Description
Header	Title
Paragraph	Text

alignements

| Left        |    Center   |         Right |
| :---        |    :----:   |          ---: |
| Header      | Title       | Here's this   |
| Paragraph   | Text        | And more      |

Left	Center	Right
Header	Title	Here’s this
Paragraph	Text	And more

Table are often data structure difficult to layout. For complex tables you will need to use code chunks, e.g. kable() from {knitr} with kable_styling() from {kableExtra}

Images

These coding give the same results (Markdown and HTML):

online images (Markdown and HTML)

![](https://raw.githubusercontent.com/zoometh/oxford/main/R4A/www/logo.png){width=100px}  
<img src="https://raw.githubusercontent.com/zoometh/oxford/main/R4A/www/logo.png" alt="" width=100>

local images (Markdown and HTML)

![](www/logo.png){width=100px}  
<img src="www/logo.png" alt="" width=100>

Spaces and end of lines

Extra spaces (HTML only)

&emsp; means 4 spaces (= a tabulation)
&ensp; means 2 spaces
  means 1 space

End of line (<br> in HTML) with 2 or more spaces and return, for example:

'Reconnais-toi  
Cette adorable personne c'est toi  
Sous le grand chapeau canotier  
Oeil
Nez  
Ta Bouche  
Voici l’ovale de ta figure  
Ton cou Exquis' (Apollinaire, 1913)

‘Reconnais-toi
Cette adorable personne c’est toi
Sous le grand chapeau canotier
Oeil Nez
Ta Bouche
Voici l’ovale de ta figure
Ton cou Exquis’ (Apollinaire, 1913)

Titles

# Header level 1

## Heading level 2

### Heading level 3

etc.

An anchor:

# Practice {#practice}

Avoid numbering:

#### Spaces and end of lines {-}

Avoid numbering and add an anchor:

#### Bookmarks {-#bookmarks}

Hyperlinks

to text

Report with R Markdown, part 2: [Practice](https://zoometh.github.io/oxford/R4A/2_R Markdown_Practice)
Report with R Markdown, part 2: Practice

to an image

[![](www/logo.png){width=70px}](https://www.unipi.it/index.php/humanities/item/16574-r4rchaeologists)

Hyperlinks can also be done with HTML/CSS

Bookmarks

After this theoretical part, you will have to [practice](#practice)
After this theoretical part, you will have to practice

The reference section, ‘Practice’, appears like that:

Footnotes

Footnote to the bottom of the document

A simple footnote,[^1] or a longer one.[^bignote]
A simple footnote,¹ or a longer one.²

[^1]: This is the first footnote.

[^bignote]: Here's one with multiple paragraphs and code.

    Indent paragraphs to include them in the footnote.

    `{ my code }`

    Add as many paragraphs as you like.

2.1.2 Cross-referencing

Cite and reuse variables, figures, tables, sections, etc., through your document

In the following verbatim blocks we use simple quotes ( ’ ) in replacement of the back quotes ( ` ).

Variables

library(archdata)
data("Handaxes")
number.of.axes <- nrow(Handaxes)

Variables are called like this: ‘r variable_name’

'(...) the Furze Platt dataset counts 'r number.of.axes' described by 'r ncol(Handaxes)'. The maximal length (L = 'r max(Handaxes$L)')  (...)'

‘(…) the Furze Platt dataset counts 600 described by 8. The maximal length (L = 242) (…)’

Figures

library(archdata)
data("Handaxes")
plot(Handaxes$L, Handaxes$B)
model <- lm(B ~ L, data = Handaxes)
abline(lm(model))

Figure 2.1: Maximum Length/Maximum breadth in cm

'(...) the distribution of the maximum length (L) and maximum breadth (B) shows a R^2^ = 'r round(model$coefficients[2], 2)',  Fig. \@ref(fig:maxLmaxB)) (...)'

‘(…) the distribution of the maximum length (L) and maximum breadth (B) shows a R² = 0.42, Fig. 2.1) (…)’

Sections

See section [**Bookmarks**](#bookmarks)
See section Bookmarks

2.1.3 Bibliographic references

file .bib referenced in the YAML header

rmd_yaml_bib

rmd_bib

cross citation in text

code in R Markdown	Render
`@Xie22`	Xie (2022)
`[@Xie22]`	(Xie 2022)
`[credits: @Xie22]`	(credits: Xie 2022)
`published by Yihui Xie [-@Xie20; -@Xie22]`	published by Yihui Xie (2020; 2022)
…	…

Bibliographies and citations (Xie, Dervieux, and Riederer 2020)

2.2 Code chunks

Code chunks, or chunks, are the placeholders for the coding part of the document

2.2.1 Header

The chunk header is used to set the output options (show code, size of the output image, alignement, etc.). The first top chunk (the first one in the document) allows to set these options for all other chunks, e.g. knitr::opts_chunk$set(echo = TRUE) will ‘echoing’ all chunks unless you change these options in the following headers

graphical interface for options

run the previous chunks but not this one

run this chunk

Code evaluation

include = FALSE prevents code and results from appearing in the finished file. R Markdown still runs the code in the chunk, and the results can be used by other chunks.
echo = FALSE prevents code, but not the results from appearing in the finished file. This is a useful way to embed figures.
message = FALSE prevents messages that are generated by code from appearing in the finished file.
warning = FALSE prevents warnings that are generated by code from appearing in the finished.

Graphical results

Options of the graphical results

fig.cap = "..." adds a caption to graphical results.
fig.height = 7 height to use in R for plots created by the chunk (in inches)
fig.width = 7 width to use in R for plots created by the chunk (in inches)
fig.align = default how to align graphics in the final document. One of ‘left’, ‘right’, or ‘center’
fig.pos = 'H' fix the output exactly here

2.2.2 Body

The body of a code chunk is where you place the R code you have scripted.

Images

Images can be render with knitr::include_graphics("path/to/image")

knitr::include_graphics("www/munsingen_fib_measures.png")

Figure 2.2: Fibulae measurements (Hodson, 1970)

2.3 YAML part

This is the document header, it contains the metadata (e.g, Title, Authors, date) and the document configuration (e.g. HTML or PDF rendering, table of content). It is composed on key-value pairs:

title: Title

author: Author

date:
"03/02/2022"
“03/02/2022”
"'r format(Sys.time(), '%D')'"
“01/30/23”
"'r format(Sys.time(), '%d %B %Y')'"
“30 January 2023”
…

output:
html_document
pdf_document
…
pdf_document:
toc: yes

toc: table of contents
toc: yes
toc_depth: 4
toc_float:
collapsed: no
…

bibliography: bibliographical references, BibTex format (e.g. https://github.com/zoometh/oxford/blob/main/R4A/references.bib)

…

YAML for R Markdown (Xie, Allaire, and Grolemund 2018)

3 HTML/CSS

Can be use in all parts of the document (YAML header, code chunks, narrative parts)

3.1 Styling

code in R Markdown (= HTML)	Render
`<span style='font-size: 30px'>Big font</span>`	Big font
`<b>bolded</b>`	bolded
`<span style="color:red">red</span>`	red
…	…

Customize the document with CSS layouts like <notes>this CSS element with a dodgerblue for background and white for text</notes> here: https://github.com/zoometh/oxford/blob/main/R4A/styles.css Customize the document with CSS layouts like this CSS element with a dodgerblue for background and white for text

The CSS file is here: https://github.com/zoometh/oxford/blob/main/R4A/styles.css

HTML online editor

3.2 Interactivity

The interest of HTML is its ability to be deployed online, with interactive settings. R offers a real framework to create interactive documents, Shiny. Shiny can be integrated into R Markdown

Try: File > New File > Rmarkdown > Shiny, or in the YAML header:

    runtime: shiny`

3.2.1 Maps

With the {leaflet} package

library(dplyr)
library(leaflet)
munsingen.long <- 7.569587484129203
munsingen.lat <- 46.864709895956004
leaflet(width = "60%", height = "400px") %>%
  addTiles(group = 'OSM') %>%
  addControl("Munsingen necropolis", position = "bottomright") %>%
  addProviderTiles(providers$Esri.WorldImagery, group='Esri.WorldImagery') %>%
  addMarkers(munsingen.long,
             munsingen.lat,
             label = "Munsingen necropolis") %>%
  addLayersControl(
    baseGroups = c('OSM', 'Esri.WorldImagery')) %>%
  addScaleBar(position = "bottomleft")

3.2.2 Plots 2D

With the {plotly} package

library(plotly)
library(dplyr)
library(archdata)
data("Fibulae")
Fibulae.ex <- Fibulae
Fibulae.ex$lbl <- paste0("<b>Museum num.: ", Fibulae.ex$Mno, "</b><br>",
                          "Length: ", Fibulae.ex$Length, "<br>",
                          "Foot Angle: ", Fibulae.ex$FA, "<br>")
plot_ly(data = Fibulae.ex, 
        x = ~Length,
        y = ~FA,
        text = ~lbl,
        hoverinfo = "text") %>% 
  layout(title = "Munsingen fibulae")

3.2.3 Plots 3D

With the {rgl} package

library(rgl)
options(rgl.useNULL = TRUE) # avoid the popup RGL device
nb.samp <- 12
# 12 graves with the numerous fibulae
Fibulae.nbGrave <- Fibulae %>% 
  count(Grave) %>%
  arrange(-n) %>%
  slice_head(n = nb.samp)
Fibulae.samp <- Fibulae[Fibulae$Grave %in% Fibulae.nbGrave$Grave, ]
# rainbow colors by graves
Fibulae.samp$color <- rainbow(nb.samp)[as.numeric(as.factor(Fibulae.samp$Grave))]
plot3d(
  x = Fibulae$Length,
  y = Fibulae$FA,
  z = Fibulae$BH, 
  col = Fibulae.samp$color, 
  type = 's', 
  xlab = "Length", 
  ylab  ="Foot Angle",
  zlab = "Bow Height")
rglwidget()

3D scatterplots

4 Export document

Export R Markdown in: HTML, PDF, LaTeX, Word, ODT, RTF, Markdown, etc. (see: https://rmarkdown.rstudio.com/lesson-9.html)

4.1 HTML

Basic. HTML export is the default option of a R Markdown document.

4.2 PDF

Harder. PDF uses LaTeX syntax, if you don’t have MiKTeX installed, you need to install the {tinytex} package [Xie19].

install.packages('tinytex')
tinytex::install_tinytex()
# .rs.restartR()

To export in PDF, change the YAML key-value pair bookdown::html_document2: to bookdown::pdf_document2: and knit. These temporary files are creates:

At the end of the render these files are deleted

4.3 LaTeX

LaTeX (extension of TeX) is a rich plain text syntax for academic writing. To export in TeX, select in the YAML header a PDF export + keep tex:

    bookdown::pdf_document2: 
        keep_tex: true

Alongside Pandoc, exists a lot of online apps making the conversions easier (e.g. Word to HTML)

5 Publishing on platforms

Rpubs
- after Render:
GitHub/GitLab, the same document is accessible by different means:
- formatted: https://github.com/zoometh/oxford/blob/main/R4A/helloworld.html
- raw: https://raw.githubusercontent.com/zoometh/oxford/main/R4A/helloworld.html
- HTML: https://zoometh.github.io/oxford/R4A/helloworld.html
- downloadable: see below

6 Practice

1) Use 1_Rmarkdown_Theory.Rmd as a model (copy/paste code snippets, Mardown syntax, etc.):

2) 2_Rmarkdown_Practice.Rmd gives an example of the desired structure for the Practice part:

3) references.bibis the document where you will add the bibliographic references of the practice part. Google Scholar is a nice tool to copy/paste BibTex references, e.g. this reference:

4) choose a dataset of those available in the {archdata} package (e.g. ‘Handaxes’), you will have to analyse these data/reuse the code you have already created (run ?archdata to see the list of these dataset)

References

Xie, Yihui. 2022. Knitr. Elegant, Flexible, and Fast Dynamic Report Generation with r. https://yihui.org/knitr/.

Xie, Yihui, Joseph J Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. https://bookdown.org/yihui/rmarkdown/; CRC Press.

Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook/.

This is the first footnote.↩︎
Here’s one with multiple paragraphs and code.

Indent paragraphs to include them in the footnote.

{ my code }

Add as many paragraphs as you like.↩︎

Report with R Markdown ¶ ¶ Report data analysis with R Markdown authoring framework ¶ ¶ Theory

Thomas Huet, University of Oxford

January 2023

1 Introduction

1.1 Create a new document

1.2 Navigate

1.2.1 Visual R Markdown

2 Document structure

2.1 Narrative parts

2.1.1 Markdown syntax

Styling text

Lists

Tables

Images

Spaces and end of lines

Titles

Hyperlinks

Bookmarks

Footnotes

2.1.2 Cross-referencing

Variables

Figures

Sections

2.1.3 Bibliographic references

2.2 Code chunks

2.2.1 Header

Code evaluation

Graphical results

2.2.2 Body

Images

2.3 YAML part

3 HTML/CSS

3.1 Styling

3.2 Interactivity

3.2.1 Maps

3.2.2 Plots 2D

3.2.3 Plots 3D

4 Export document

4.1 HTML

4.2 PDF

4.3 LaTeX

5 Publishing on platforms

6 Practice

References

Report with R Markdown ¶ ¶
Report data analysis with R Markdown authoring framework
¶ ¶ Theory